Abundance,biomass, structure,and activity of the microbial complexes of minerotrophic and ombrotrophic peatlands

A very large microbial biomass was revealed in peat bogs by means of fluorescence microscopy. In ombrotrophic peatlands, the pool of the dry-weight microbial biomass in the 1.5-m layer constituted 3–4 t/ha and was twice as high as in the minerotrophic peat bogs. Fungal biomass was predominant (55–99%) in ombrotrophic peatlands, while bacterial biomass predominated (55–86%) in minerotrophic peatlands. In ombrotrophic peatlands, the microbial biomass was concentrated in the upper layers, while in minerotrophic peatlands, it was uniformly distributed in the bulk. After drainage, the microbial pool in the ombrotrophic peatlands increased twofold; that in the minerotrophic peatlands remained at the same level. The potential activity of nitrogen fixation and denitrification was revealed across the whole profile of the peatlands. The average values of these potential activities were five times higher in the minerotrophic peatlands, where bacterial biomass predominated.     

Abundance, biomass, structure, and activity of the microbial complexes of minerotrophic and ombrotrophic peatlands

Very large microbial biomass was revealed in peat bogs by means of fluorescence microscopy. In ombrotrophic peatlands, the pool of the dry-weight microbial biomass in the 1.5-m layer constituted 3-4 t/ha and was twice as high as in the minerotrophic peat bogs. Fungal biomass was predominant (55-99%) in ombrotrophic peatlands, while bacterial biomass predominated in minerotrophic peatlands (55-86%). In ombrotrophic peatlands, the microbial biomass was concentrated in the upper layers, while in minerotrophic peatlands, it was uniformly distributed in the bulk. After drainage, the microbial pool in the ombrotrophic peatlands increased twofold; that in the minerotrophic peatlands remained at the same level. The potential activity of nitrogen fixation and denitrification was revealed across the whole profile of the peatlands. The average values of these potential activities were five times higher in the minerotrophic peatlands, where bacterial biomass predominated.     

Quality assessment of compost prepared from fly ash and crop residue

Fly ash was co-composted with wheat straw and 2% rock phosphate (w/w) for 90 days and different chemical and microbiological parameters monitored to evaluate its effect on the composting process. Fly ash addition at 20% level resulted in the lowest C/N of 16.4:1 and highest available and total phosphorus. Increasing the addition of fly ash from 40 to 60% (w/w) did not exert any detrimental effect on either C:N or the microbial population.     

Organic matter transformation and detoxification in dry olive mill residue by the saprophytic fungus Paecilomyces farinosus

Dry olive mill residue (DOR), the by-product of the two-phase extraction process, is very rich in organic matter and nutritionally relevant cations. For this reason, the agronomic use of this waste has been suggested although DOR exhibits significant phytotoxicity. The objective of this study was to investigate the impact of Paecilomyces farinosus on both organic matter modification and detoxification of this waste. Humification ratio in DOR colonized by the fungus for 20 weeks was increased by about 65% with respect to the abiotic control and humification index reached 0.38, a value that characterizes well-humified materials. High performance size-exclusion chromatography of humic acids from fungal cultures showed a marked increase in both weight-averaged and number-averaged molecular weights with respect to abiotic controls. Water-soluble phenols were reduced by 45% in 20-week-old P. farinosus cultures on DOR and mass-balance ultra-filtration showed that the relative abundance of the molecular weight fraction of phenols above 30 kDa increased from 31 to 72% suggesting the occurrence of polymerization. Experiments performed with alfalfa grown on soils containing 2.5% (w/w) of abiotic controls and fungal-treated DOR showed that phytotoxicity was totally suppressed in the waste that underwent fungal treatment.     

The role of Eriophorum vaginatum in CH4 flux from an ombrotrophic peatland

Vegetation composition was found to be an important factor controlling CH₄ emission from an ombrotrophic peatland in the UK, with significantly greater (P < 0.01) CH₄ released from areas containing both Eriophorum vaginatumL. and Sphagnum, than from similar areas without E. vaginatum. Positive correlations were observed between the amount of E. vaginatum and CH₄ emission, with the best predictor of flux being the amount of below-ground biomass of this species (r ² = 0.93). A cutting experiment revealed that there was no significant difference (P > 0.05) in CH₄ flux between plots with E. vaginatum stems cut above the water table and plots with intact vegetation, yet there was a 56% mean reduction in CH₄ efflux where stems were cut below the water table (P < 0.05). The effect of E. vaginatum on CH₄ release was mimicked by the presence of inert glass tubes. These findings suggest that the main short-term role of E. vaginatum in the ecosystem is simply as a conduit for CH₄ release. The longer-term importance of E. vaginatum in controlling CH₄ fluxes through C substrate input was suggested by the positive correlation between the night-time CO₂ and CH₄ fluxes (r ² = 0.70), which only occurred when the vegetation was not senescent. This revised version was published online in June 2006 with corrections to the Cover Date.     

Protein self-marking by emerald ash borer: an evaluation of efficacy and persistence

Understanding the dispersal ability of invasive insects provides useful insights for developing effective management strategies. Historically, methods for marking insects for dispersal studies have been expensive, time-consuming, labor-intensive, and oftentimes ineffective, especially for woodboring beetles. Also, capturing or rearing insects requires human handling, which can alter behavior. Protein immunomarking is a well-established technique for studying the dispersal of insects; however, it has not been applied to woodborers. This study evaluates the potential for using protein immunomarkers applied directly to woodborer-infested trees to mark emerging beetles. Specifically, in the first experiment, we sprayed varying concentrations of ovalbumin (egg white) solution directly onto logs infested with emerald ash borer (EAB), Agrilus planipennis Fairmaire (Coleoptera: Buprestidae, Agrilini). In turn, an enzyme-linked immunosorbent assay was used to detect the presence of protein on emerged beetles. To test the persistence of the mark, we applied varying concentrations of albumin to freeze-killed beetles, mounted them on pins, and placed them over various time intervals in an exposed location outdoors. Adult EAB self-marked as they emerged from protein-treated trees, with higher protein concentrations persisting for longer on the cuticle. This technique offers a convenient, inexpensive, and durable means of marking woodborers and circumvents the need for human handling, allowing for more natural behavior and more realistic estimates of dispersal. Protein self-marking may find application in studies of woodborer dispersal within natural forest environments.     

Organic matter composition of gravel-stored sediments from salmon-bearing streams

The objective of this project was to evaluate the changing composition and structure of the sediment-associated organic matter (OM) stored in the gravel bed of highly productive salmon-bearing streams and, determine if the OM changes affect the morphology and settling rates of the sediment. In July of 2001, a dozen infiltration gravel bags were buried in the channel bed of O'Ne-eil Creek in northern British Columbia (Canada) to collect fine sediment and the associated organic matter for chemical and morphological analysis. The bags were removed over a 10 week period which incorporated summer low flows, salmon spawning, salmon die-off and the onset of autumn low flow conditions. Our results indicate two visibly different structures in the organic matter film overlying the mineral material of the flocs. A web-like structure was noted during mid-spawn while a film-like covering was observed in pre-spawn and post-fish periods. The strength of the film-like covering is surmised to be associated with the larger gravel-stored floc sizes noted at these times. Chemical analysis of these biofilms indicated higher metal complexation properties during the spawning periods as opposed to before or after salmon were present. The changing OM contributions were associated with changes in floc size, density and settling rates. The physical disturbance to the gravels associated with spawning salmon was also correlated with altered characteristics of the gravel-stored flocs.     

Organic matter distribution and retention along transects from hilltop to kettle hole within an agricultural landscape

In agricultural landscapes, the spatio-temporal distribution of organic matter (OM) varies greatly across landscape structures and soil types. We investigated patterns of organic carbon (OC) content, polyvalent cations, and isotopic values for specific OM fractions along transects spanning topographic positions from erosional to depositional areas, including aquatic sediments within a single kettle hole. We hypothesized different drivers exist at different scales. At the transect scale, we hypothesized (1) landscape form and land management to explain patterns of isotopic and OC content from different OM fractions. At the aggregate scale, (2) we expected different OM-mineral associations to explain stabilized OM. We also hypothesized, (3) that shallow sediment δ¹³C and δ¹⁵N of the kettle hole reflected different terrestrial sources. We found that distinct differences in the OM turnover rates existed between the fractions suggesting that different processes are affecting the transformation rates that are recorded in the isotopic composition patterns. Erosion along with plant productivity drive mineral-associated fractions over the transect, while microbial decomposition and slurry influence freely available and aggregated OM fractions. The type and magnitude of OM-mineral associations changed along the transect while binding OM of different decomposition status. OM in mineral-associated fractions in kettle hole sediments were derived from clay- and silt-sized particles from the field, whereas OM in freely available and aggregated fractions potentially originated from macrophytes. We conclude that kettle holes constitute important sinks for terrestrial OM across the landscape.     

Technical note: evaluation of extraction methodologies for the determination of an organochlorine pesticide residue in vegetation

Numerous extraction methodologies are used to quantify pesticide levels in vegetation. Sample availability, resource use, efficiency, time consumption, space allocation, and cost vary considerably among the commonly employed techniques. A study was conducted to compare the efficiency of microwave assisted extraction (MAE), blender homogenized extraction (BE), Soxhlet extraction (SE), the QuEChERS ("Quick, Easy, Cheap, Effective, Rugged, and Safe") method, and a simple oven assisted extraction (OAE), to recover p,p'-DDE from the tissues of Cucurbita pepo. A hot-solvent soak of stem or root tissues in a 2-propanol/hexane mixture, OAE yields recoveries that are statistically equivalent to the other procedures. The method recovered 1800 +/- 190 ng g(-1) and 8100 +/- 900 ng g(-1) (BCF = 87 +/- 9.7) p,p'-DDE from stem and root tissue, respectively. Recoveries for the other methods ranged from 1400-2200 ng g(-1) for the stems and 3600-7200 ng g(-1) for the roots. Statistical analyses for stem and root extraction indicate that there is no significant difference among the variances of each method. Given its simplicity, precision, and efficiency, OAE appears to be suitable for the extraction of an organic pollutant such as p,p'-DDE from plant tissues and for use in phytotechnology development and risk assessment.     

Decadal losses of canopy‐forming algae along the warm temperate coastline of Brazil

The loss of canopy‐forming seaweeds from urbanized coasts has intensified in response to warming seas and non‐climatic pressures such as population growth and declining water quality. Surprisingly, there has been little information on the extent of historical losses in the South‐western Atlantic, which limits our ability to place this large marine ecosystem in a global context. Here, we use meta‐analysis to examine long‐term (1969–2017) changes to the cover and biomass of Sargassum spp. and structurally simple algal turfs along more than 1,000 kilometres of Brazil's warm temperate coastline. Analysis revealed major declines in canopy cover that were independent of season (i.e., displaying similar trends for both summer and winter) but varied with coastal environmental setting, whereby sheltered bays experienced greater losses than coastal locations. On average, covers of Sargassum spp. declined by 2.6% per year, to show overall losses of 52% since records began (ranging from 20% to 89%). This contrasted with increases in the cover of filamentous turfs (24% over the last 27 years) which are known to proliferate along human‐impacted coasts. To test the relative influence of climatic versus non‐climatic factors as drivers of this apparent canopy‐to‐turf shift, we examined how well regional warming trends (decadal changes to sea surface temperature) and local proxies of coastal urbanization (population density, thermal pollution, turbidity and nutrient inputs) were able to predict the changes in seaweed communities. Our results revealed that the most pronounced canopy losses over the past 50 years were at sites exhibiting the greatest degree of coastal warming, the highest population growth and those located in semi‐enclosed sheltered bays. These findings contribute knowledge on the drivers of canopy loss in the South‐western Atlantic and join with global efforts to understand and mitigate declines of marine keystone species.     

Organic matter mineralization with the reduction of ferric iron: A review

A review of the literature indicates that numerous microorganisms can reduce ferric iron during the metabolism of organic matter. In most cases, the reduction of ferric iron appears to be enzymatically catalyzed and, in some instances, may be coupled to an electron transport chain that could generate ATP. However, the physiology and biochemistry of ferric iron reduction are poorly understood. In pure culture, ferric iron‐reducing organisms metabolize fermentable substrates, such as glucose, primarily to typical fermentation products, and transfer only a minor portion of the electron equivalents in the fermentable substrates to ferric iron. However, fermentation products, especially hydrogen and acetate, may be important electron donors for ferric iron reduction in natural environments. The ability of some organisms to couple the oxidation of fermentation products to the reduction of ferric iron means that it is possible for a food chain of iron‐reducing organisms to completely mineralize nonrecalcitrant organic matter with ferric iron as the sole electron acceptor. The rate and extent of ferric iron reduction depend on the forms of ferric iron that are available. Most of the ferric iron in sediments is resistant to microbial reduction. Ferric iron‐reducing organisms can exclude sulfate reduction and methane production from the zone of ferric iron reduction in sediments by outcompeting sulfate‐reducing and methanogenic food chains for organic matter when ferric iron is available as amorphic ferric oxyhydroxide. There are few quantitative estimates of the rates of ferric iron reduction in natural environments, but there is evidence that ferric iron reduction can be an important pathway for organic matter decomposition in some environments. There is a strong need for further study on all aspects of microbial reduction of ferric iron.     

RSARF: prediction of residue solvent accessibility from protein sequence using random forest method

Prediction of protein structure from its amino acid sequence is still a challenging problem. The complete physicochemical understanding of protein folding is essential for the accurate structure prediction. Knowledge of residue solvent accessibility gives useful insights into protein structure prediction and function prediction. In this work, we propose a random forest method, RSARF, to predict residue accessible surface area from protein sequence information. The training and testing was performed using 120 proteins containing 22006 residues. For each residue, buried and exposed state was computed using five thresholds (0%, 5%, 10%, 25%, and 50%). The prediction accuracy for 0%, 5%, 10%, 25%, and 50% thresholds are 72.9%, 78.25%, 78.12%, 77.57% and 72.07% respectively. Further, comparison of RSARF with other methods using a benchmark dataset containing 20 proteins shows that our approach is useful for prediction of residue solvent accessibility from protein sequence without using structural information. The RSARF program, datasets and supplementary data are available at http://caps.ncbs.res.in/download/pugal/RSARF/.     

Organic matter mineralization in an organic-rich sediment: Experimental stimulation of sulfate reduction by fish food pellets

Abstract The combined effects of organic matter additions and temperature on short chain fatty acid (SCFA) turnover, sulfate reduction and nutrient accumulation were examined in an organic-rich fish farm sediment. Fish food pellets, which contribute significantly to the organic matter loss from fish farms, were added to surface sediment at three loadings (2.8; 14.0; 28.0 mg ww g⁻¹ ww sediment; equivalent to organic matter loadings measured during fish farming) and incubated for 30 days in anaerobic bags at 5°C and 15°C. SCFA accumulated to high levels (acetate up to 85 mM, propionate up to 17 mM, butyrate up to 25 mM) in sediments amended with food pellets, and sulfate reduction was stimulated up to 30 times relative to unamended sediments. Sulfate reducers appeared saturated with substrates (SCFA) even in the lowest additions. A low C/N ratio (0.4–1.8) of the major mineralization products (TCO₂ and NH₄⁺) indicated preferential nitrogen mineralization in amended sediment compared with the total particulate pool (C/N = 8.8–11.9) and added food pellets (C/N = 8.4).     

Conservation of temperate forest birds in Chile: implications from the study of an isolated forest relict

We characterize the bird assemblage of an isolated relict temperaterainforest (Santa Inés) in terms of its structure, composition anddynamics. The relict character and long-term isolation of this forest remnant,immersed in a matrix of semiarid scrub, provide a natural experiment to assessthe consequences of long-term isolation and forest area reduction for temperatebird species. Bird surveys were conducted in a forest fragment and thesurrounding scrub matrix between April 1999 (austral autumn) and October 2000(austral spring) on a seasonal basis. Within the forest fragment wedistinguished two microhabitat types: creeks and areas far from creeks (i.e.slopes). A total of 36 species were recorded in the study site, of which 21were inside the relict forest. Highest bird abundance and richness wererecorded during winter and spring, and these were always higher in creek plotsrather than slope plots. Comparisons between this assemblage and thosedistributed in the continuous temperate forest (located more than 900km southwards) indicate that this bird assemblage shares moresimilarities, with regard to bird species composition, to southern temperateforest localities and to other relict forests, than to nearer scrub habitats.However, there are eight species, endemic to temperate forests in southern SouthAmerica, missing from our system. In this regard, our analyses indicate thatthese eight endemic species should be of great conservation concern and willlikely be the ones that will go extinct first if the fragmentation of thetemperate forest continues.     

Low‐severity fire as a mechanism of organic matter protection in global peatlands: Thermal alteration slows decomposition

Worldwide, regularly recurring wildfires shape many peatland ecosystems to the extent that fire‐adapted species often dominate plant communities, suggesting that wildfire is an integral part of peatland ecology rather than an anomaly. The most destructive blazes are smoldering fires that are usually initiated in periods of drought and can combust entire peatland carbon stores. However, peatland wildfires more typically occur as low‐severity surface burns that arise in the dormant season when vegetation is desiccated, and soil moisture is high. In such low‐severity fires, surface layers experience flash heating, but there is little loss of underlying peat to combustion. This study examines the potential importance of such processes in several peatlands that span a gradient from hemiboreal to tropical ecozones and experience a wide range of fire return intervals. We show that low‐severity fires can increase the pool of stable soil carbon by thermally altering the chemistry of soil organic matter (SOM), thereby reducing rates of microbial respiration. Using X‐ray photoelectron spectroscopy and Fourier transform infrared, we demonstrate that low‐severity fires significantly increase the degree of carbon condensation and aromatization of SOM functional groups, particularly on the surface of peat aggregates. Laboratory incubations show lower CO₂ emissions from peat subjected to low‐severity fire and predict lower cumulative CO₂ emissions from burned peat after 1–3 years. Also, low‐severity fires reduce the temperature sensitivity (Q₁₀) of peat, indicating that these fires can inhibit microbial access to SOM. The increased stability of thermally altered SOM may allow a greater proportion of organic matter to survive vertical migration into saturated and anaerobic zones of peatlands where environmental conditions physiochemically protect carbon stores from decomposition for thousands of years. Thus, across latitudes, low‐severity fire is an overlooked factor influencing carbon cycling in peatlands, which is relevant to global carbon budgets as climate change alters fire regimes worldwide.